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Crystal structure of (–)-(R,E)-3-(1,3-benzodioxol-5-yl)-5-[(4S,5R)-5-hy­dr­oxy­methyl-2,2-di­methyl-1,3-dioxolan-4-yl]-N,N-di­methyl­pent-4-enamide

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aSchool of Medicine, Keio University, Hiyoshi 4-1-1, Kohoku-ku, Yokohama 223-8521, Japan, and bDepartment of Applied Chemistry, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, Yokohama 223-8522, Japan
*Correspondence e-mail: oec@keio.jp

Edited by H. Ishida, Okayama University, Japan (Received 26 April 2018; accepted 11 May 2018; online 18 May 2018)

In the title compound, C20H27NO6, the amide moiety is essentially planar, with a maximum deviation of 0.073 (3) Å, and one of the N-methyl groups shows rotational disorder. The five-membered 1,3-dioxolane ring adopts an envelope form, with the C atom bonded to the olefin side chain as the flap, which deviates from the mean plane through the other four atoms by 0.564 (7) Å. The 1,3-dioxole ring fused to the benzene ring adopts a flattened envelope form, with the C atom between the two O atoms as the flap, which deviates from the mean plane through the other four atoms by 0.215 (7) Å. The C—C=C—C olefin moiety is essentially planar and makes a dihedral angle of 87.1 (3)° with the benzene ring. An intra­molecular O—H⋯O hydrogen bond supports the mol­ecular conformation, enclosing an S(11) graph-set motif. In the crystal, inter­molecular C—H⋯O hydrogen bonding links the mol­ecules into a tape running along the b axis. Furthermore, other weak C—H⋯O hydrogen bonds and a C—H⋯π inter­action connect the tapes into a sheet structure parallel to (100).

1. Chemical context

Five-membered cyclic acetal is a pervasive building block in organic synthesis since it is easily prepared from an aliphatic or an aromatic 1,2-diol. These conversions are often carried out with protection of the contiguous diol (Wuts, 2014[Wuts, P. G. M. (2014). Green's Protective Groups in Organic Synthesis, 5th ed., pp. 385-456, 465-468 and 545-552. New York: John Wiley & Sons Inc.]) to prevent unexpected side reactions or to reduce the polarity of the substrate, especially for carbohydrates. Although masking of the hy­droxy groups is a disadvantage in terms of crystallization, due to loss of hydrogen-bond donors, it is expected to stabilize the crystal packing in order to contribute conformational rigidity by forming the cyclic acetal (Vijayasaradhi et al., 2003[Vijayasaradhi, S., Aidhen, I. S. & Varghese, B. (2003). Carbohydr. Res. 338, 2899-2903.]).

[Scheme 1]

The title compound is an inter­mediate in the total synthesis of a natural alkaloid (Ishii et al., 2018[Ishii, K., Seki, Y., Ishibashi, M., Sato, T. & Chida, N. (2018). preparation.]) possessing both 1,3-dioxolane and 1,3-benzodioxole components. The relative configurations were confirmed by the X-ray analysis as C7R, C10S and C14R.

2. Structural commentary

The mol­ecular structure of the title compound is shown in Fig. 1[link]. The amide moiety (C1/O2/N3/C4–C6) is essentially planar, with a maximum deviation of 0.073 (8) Å at atom C4. One of the N-methyl groups (C4) shows rotational disorder over two orientations, with refined occupancies of 0.54 (8) and 0.46 (8). The 1,3-dioxolane ring (C10/O11/C12/O13/C14) adopts an envelope form, with puckering parameters of Q(2) = 0.362 (5) Å and φ(2) = 40.6 (7)°. The flap atom C10 deviates from the mean plane through the other four atoms by 0.564 (7) Å. The 1,3-dioxole ring (C23/C24/O25/C26/O27) in benzodioxole adopts a flattened envelope form, with puckering parameter of Q(2) = 0.135 (5) Å and φ(2) = 326 (2)°. The flap atom C26 deviates from the mean plane through the other four atoms by 0.215 (7) Å. The olefin moiety (C7—C8=C9—C10) is essentially planar and makes a dihedral angle of 87.1 (3)° with the benzene ring (C19–C24). An intra­molecular O—H⋯O hydrogen bond (O16—H16⋯O2; Table 1[link]) supports the mol­ecular conformation, generating an S(11) graph-set motif.

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C19–C24 benzene ring.

D—H⋯A D—H H⋯A DA D—H⋯A
O16—H16⋯O2 0.84 1.99 2.810 (5) 166
C14—H14⋯O13i 1.00 2.43 3.253 (6) 139
C5—H5A⋯O16ii 0.98 2.55 3.417 (7) 147
C22—H22⋯O2iii 0.95 2.55 3.417 (5) 152
C21—H21⋯Cgiv 0.95 2.98 3.794 (4) 145
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z]; (ii) x, y+1, z; (iii) [-x+1, y+{\script{1\over 2}}, -z+1]; (iv) [-x+1, y-{\script{1\over 2}}, -z+1].
[Figure 1]
Figure 1
The mol­ecular structure of the title compound, with the atom labelling. Displacement ellipsoids are drawn at the 50% probability levels. A yellow dotted line indicates the intra­molecular O—H⋯O hydrogen bond. Only H atoms connected to O and chiral C atoms are shown for clarity.

3. Supra­molecular features

The crystal packing is stabilized by a C—H⋯O inter­action (C14—H14⋯O13i; symmetry code as in Table 1[link]), which links the mol­ecules into a tape running along the b axis, with a C(3) graph-set motif. Furthermore, other weak C—H⋯O hydrogen bonds and a C—H⋯π inter­action (C5—H5A⋯O16ii, C22—H22⋯O2iii and C21—H21⋯Cgiv; Cg is the centroid of the C19–C24 benzene ring; Table 1[link]) connect the tapes into a sheet parallel to (100) (Figs. 2[link] and 3[link]).

[Figure 2]
Figure 2
The crystal packing of the title compound, viewed down the a axis, showing the sheet structure parallel to (100). Black dashed lines indicate inter­molecular C—H⋯O and C—H⋯π inter­actions. Cg (green sphere) is the centroid of the C19–C24 benzene ring. Only H atoms involved in the above inter­actions are shown for clarity. [Symmetry codes: (i) −x + 1, y + [{1\over 2}], −z; (ii) x, y + 1, z; (iii) −x + 1, y + [{1\over 2}], −z + 1; (iv) −x + 1, y[{1\over 2}], −z + 1.]
[Figure 3]
Figure 3
The crystal packing of the title compound, viewed down the b axis, showing layered sheet structures parallel to (100). Black dashed lines indicate inter­molecular C—H⋯O and C—H⋯π inter­actions. Cg (green sphere) is the centroid of the C19–C24 benzene ring. Only H atoms involved in the above inter­actions are shown for clarity.

4. Database survey

In the Cambridge Structural Database (CSD, Version 5.39, last update February 2018; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]), 32 structures are registered which contain a skeleton with a combination of benzodioxole and N,N-di­methyl­amide components, (a), similar to the title compound (Fig. 4[link]). These include 12 structures with no other substituent on the 1,3-benzodioxole; the 1,3-dioxole rings in eight structures adopt envelope forms similar to the title compound, while those in three structures show planar (one structure has no geometrical details in the CIF).

[Figure 4]
Figure 4
The core structures for the database survey, showing (a) 3-(1,3-benzodioxol-5-yl)-N,N-di­methyl­penta­namide, (b) 5-[3-(2,2-dimethyl-5-oxymethyl-1,3-dioxolan-4-yl)prop-2-en-1-yl]-1,3-benzodioxole and (c) 5-(2,2-dimethyl-5-oxymethyl-1,3-dioxolan-4-yl)-N,N-di­methyl­pent-4-en­amide.

On the other hand, searching the CSD for a structure with a combination of benzodioxole and oxymethyl­dioxolane components, (b), gives two entries with refcodes YERGUX (Doyle et al., 1994[Doyle, T. J., VanDerveer, D. & Haseltine, J. (1994). Tetrahedron Lett. 36, 6197-6200.]) and ZEMKOR (Doyle et al., 1995[Doyle, T. J., Hendrix, M. & Haseltine, J. (1995). Tetrahedron Lett. 35, 8295-8298.]). The forms of the 1,3-dioxoles in these two structures resemble the title compound, with the C—O—C—C torsion angles (absolute value) being 7.2 (6) and 6.6 (7)° in YERGUX, 9.3 (7) and 10.1 (7)° in ZEMKOR, and 8.4 (5) and 9.5 (5)° in the title compound. The 1,3-dioxolane rings also show a similar conformation, with the torsion angles being 24.1 (5) and 31.3 (5)° in YERGUX, 23.1 (7) and 36.8 (7)° in ZEMKOR, and 24.8 (5) and 36.0 (5)° in the title compound. No structure with a combination of oxymethyl­dioxolane and N,N-di­methyl­amide components, (c), has yet been reported.

5. Synthesis and crystallization

The title compound was synthesized in two steps from 3,4-O-iso­propyl­idene-3-D-arabino­pyran­ose (Gelas & Horton, 1975[Gelas, J. & Horton, D. (1975). Carbohydr. Res. 45, 181-195.]), by coupling with a known benzodioxole analogue (Rotherham & Semple, 1998[Rotherham, L. W. & Semple, J. E. (1998). J. Org. Chem. 63, 6667-6672.]) and further manipulations (Ishii et al., 2018[Ishii, K., Seki, Y., Ishibashi, M., Sato, T. & Chida, N. (2018). preparation.]). Purification was carried out by silica-gel column chromatography, and colourless crystals were afforded from a di­chloro­methane solution under a toluene-saturated atmosphere by slow evaporation at ambient temperature (m.p. 409–410 K). [α]D23 −46.0° (c 1.01, CHCl3). HRMS (ESI) m/z calculated for C20H27NO6Na+ [M + Na]+: 400.1736; found: 400.1731.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The absolute configuration of the title compound was determined according to the known stereochemistries of atoms C10 and C14 derived from D-arabinose. The H atoms on one of the N-methyl groups (C4) are disordered; they were split into two sets of positions H4AC and H4DF, the refined occupancies being 0.54 (8) and 0.46 (8), respectively. C-bound H atoms were positioned geometrically, with C—H = 0.95–1.00 Å, and constrained to ride on their parent atoms, with Uiso(H) = 1.5Ueq(C) for methyl groups or 1.2Ueq(C) otherwise. The hy­droxy H atom was placed in a difference map and treated as riding, with O—H = 0.84 Å and Uiso(H) = 1.5Ueq(O). One problematic reflection ([\overline{3}],0,16) was omitted in the final refinement.

Table 2
Experimental details

Crystal data
Chemical formula C20H27NO6
Mr 377.42
Crystal system, space group Monoclinic, P21
Temperature (K) 90
a, b, c (Å) 9.2538 (6), 6.0642 (4), 17.1441 (10)
β (°) 91.475 (2)
V3) 961.75 (11)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.27 × 0.16 × 0.10
 
Data collection
Diffractometer Bruker D8 Venture
Absorption correction Multi-scan (SADABS; Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.97, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections 8906, 2900, 2454
Rint 0.046
(sin θ/λ)max−1) 0.596
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.046, 0.099, 1.07
No. of reflections 2900
No. of parameters 250
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.25, −0.25
Computer programs: APEX3 (Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT2014 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]), publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010) and PLATON (Spek, 2009).

(–)-(R,E)-3-(1,3-Benzodioxol-5-yl)-5-{(4S,5R)-5-hydroxymethyl-2,2-dimethyl-1,3-dioxolan-4-yl}-N,N-dimethylpent-4-enamide top
Crystal data top
C20H27NO6Dx = 1.303 Mg m3
Mr = 377.42Melting point = 409–410 K
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
a = 9.2538 (6) ÅCell parameters from 3257 reflections
b = 6.0642 (4) Åθ = 2.5–24.9°
c = 17.1441 (10) ŵ = 0.10 mm1
β = 91.475 (2)°T = 90 K
V = 961.75 (11) Å3Prism, colorless
Z = 20.27 × 0.16 × 0.10 mm
F(000) = 404
Data collection top
Bruker D8 Venture
diffractometer
2900 independent reflections
Radiation source: fine-focus sealed tube2454 reflections with I > 2σ(I)
Multilayered confocal mirror monochromatorRint = 0.046
Detector resolution: 7.4074 pixels mm-1θmax = 25.1°, θmin = 2.4°
φ and ω scansh = 1111
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
k = 67
Tmin = 0.97, Tmax = 0.99l = 2020
8906 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.099H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + 1.1579P]
where P = (Fo2 + 2Fc2)/3
2900 reflections(Δ/σ)max < 0.001
250 parametersΔρmax = 0.25 e Å3
1 restraintΔρmin = 0.25 e Å3
Special details top

Experimental. IR (film): 3423, 2985, 2934, 1631, 1488, 1245, 1039 cm-1; 1H NMR (500 MHz, CDCl3): δ (p.p.m.) 6.74 (d, J = 8.0 Hz, 1H), 6.70 (d, J = 1.7 Hz, 1H), 6.67 (dd, J = 8.0, 1.7 Hz, 1H), 5.92 (s, 2H), 5.91 (ddd, J = 15.5, 7.7, 0.9 Hz, 1H), 5.59 (ddd, J = 15.5, 8.0, 0.9 Hz, 1H), 4.65 (ddd, J = 8.0, 6.6, 0.9 Hz, 1H), 4.21 (ddd, J = 7.8, 6.6, 4.9 Hz, 1H), 3.87 (dddd, J = 8.3, 7.7, 6.3, 0.9 Hz, 1H), 3.65 (dd, J = 11.5, 7.8 Hz, 1H), 3.53 (dd, J = 11.5, 4.9 Hz, 1H), 3.05 (bs, 1H), 2.97 (s, 3H), 2.92 (s, 3H), 2.69 (dd, J = 15.8, 8.3 Hz, 1H), 2.65 (dd, J = 15.8, 6.3 Hz, 1H), 1.44 (s, 3H), 1.34 (s, 3H) 13C NMR (125 MHz, CDCl3): δ (p.p.m.) 171.5 (C), 147.9 (C), 146.3 (C), 137.2 (CH), 137.0 (C), 125.7 (CH), 120.4 (CH), 108.5 (CH), 108.5 (C), 108.0 (CH), 101.1 (CH2), 78.5 (CH), 78.0 (CH), 61.2 (CH2), 44.3 (CH), 39.5 (CH2), 37.4 (CH3), 35.7 (CH3), 27.9 (CH3), 25.2 (CH3)

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
C10.7840 (5)0.4010 (8)0.3009 (2)0.0229 (11)
O20.7683 (3)0.1982 (5)0.30040 (17)0.0241 (8)
N30.9032 (4)0.4967 (7)0.2740 (2)0.0264 (10)
C41.0102 (5)0.3627 (10)0.2343 (3)0.0399 (14)
H4A1.10590.38720.25850.06*0.54 (8)
H4B1.01190.40470.17910.06*0.54 (8)
H4C0.98450.20650.23860.06*0.54 (8)
H4D1.07760.45950.20740.06*0.46 (8)
H4E0.9610.26640.19610.06*0.46 (8)
H4F1.06370.27260.27260.06*0.46 (8)
C50.9320 (5)0.7318 (9)0.2772 (3)0.0392 (14)
H5A0.90380.79940.22720.059*
H5B1.03530.75640.28770.059*
H5C0.87620.79850.31890.059*
C60.6671 (5)0.5503 (8)0.3324 (3)0.0231 (11)
H6A0.65360.6780.2970.028*
H6B0.69910.60730.38410.028*
C70.5221 (5)0.4312 (8)0.3404 (2)0.0203 (11)
H70.54010.29450.37180.024*
C80.4522 (4)0.3634 (8)0.2637 (2)0.0196 (10)
H80.36360.2850.26670.024*
C90.4993 (5)0.3999 (8)0.1930 (2)0.0196 (10)
H90.58620.48190.18870.024*
C100.4268 (5)0.3224 (8)0.1190 (2)0.0226 (11)
H100.4110.45030.08290.027*
O110.2905 (3)0.2221 (6)0.13541 (17)0.0267 (8)
C120.2523 (5)0.0853 (9)0.0707 (3)0.0293 (12)
O130.3853 (3)0.0390 (6)0.03211 (17)0.0307 (8)
C140.5029 (5)0.1354 (8)0.0758 (3)0.0226 (11)
H140.57450.19880.03930.027*
C150.5753 (5)0.0380 (8)0.1267 (3)0.0285 (12)
H15A0.51740.06240.17370.034*
H15B0.57940.17890.09770.034*
O160.7180 (4)0.0271 (7)0.14982 (19)0.0412 (10)
H160.71710.08090.1950.062*
C170.1518 (5)0.2026 (10)0.0138 (3)0.0397 (14)
H17A0.05890.22920.03830.06*
H17B0.13650.11090.03270.06*
H17C0.19460.34370.00110.06*
C180.1877 (6)0.1273 (10)0.1010 (3)0.0411 (14)
H18A0.25550.19550.13870.062*
H18B0.16950.22860.05730.062*
H18C0.09660.09490.12650.062*
C190.3611 (5)0.7677 (8)0.3512 (3)0.0244 (11)
H190.38630.81030.30.029*
C200.4189 (4)0.5773 (8)0.3858 (2)0.0193 (10)
C210.3817 (4)0.5197 (8)0.4614 (2)0.0217 (11)
H210.42230.39070.48450.026*
C220.2856 (5)0.6487 (8)0.5039 (3)0.0262 (12)
H220.25980.60910.55540.031*
C230.2304 (4)0.8334 (9)0.4685 (2)0.0223 (11)
C240.2668 (5)0.8908 (8)0.3937 (3)0.0248 (11)
O250.1991 (3)1.0850 (6)0.37196 (19)0.0325 (9)
C260.0979 (5)1.1294 (9)0.4323 (3)0.0329 (13)
H26A0.00191.09760.41340.039*
H26B0.10341.28630.44810.039*
O270.1358 (4)0.9890 (6)0.49743 (18)0.0340 (9)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.024 (3)0.029 (3)0.016 (2)0.004 (2)0.0004 (19)0.002 (2)
O20.0264 (18)0.019 (2)0.0266 (18)0.0065 (16)0.0026 (14)0.0004 (15)
N30.020 (2)0.021 (2)0.039 (2)0.0047 (19)0.0074 (18)0.002 (2)
C40.026 (3)0.040 (4)0.054 (3)0.010 (3)0.013 (3)0.004 (3)
C50.023 (3)0.032 (3)0.063 (4)0.003 (3)0.006 (3)0.000 (3)
C60.026 (2)0.021 (3)0.022 (2)0.002 (2)0.0007 (19)0.003 (2)
C70.020 (2)0.019 (3)0.022 (2)0.003 (2)0.0036 (19)0.002 (2)
C80.016 (2)0.017 (3)0.026 (2)0.002 (2)0.0001 (19)0.004 (2)
C90.020 (2)0.016 (3)0.023 (2)0.001 (2)0.0035 (19)0.004 (2)
C100.025 (3)0.022 (3)0.021 (2)0.001 (2)0.0038 (19)0.003 (2)
O110.0209 (17)0.033 (2)0.0267 (18)0.0023 (16)0.0037 (13)0.0100 (16)
C120.029 (3)0.034 (3)0.025 (3)0.000 (3)0.002 (2)0.009 (2)
O130.0283 (18)0.035 (2)0.0285 (18)0.0009 (17)0.0008 (14)0.0128 (17)
C140.025 (3)0.023 (3)0.020 (2)0.000 (2)0.0027 (19)0.004 (2)
C150.034 (3)0.024 (3)0.028 (3)0.005 (2)0.002 (2)0.006 (2)
O160.034 (2)0.052 (3)0.037 (2)0.014 (2)0.0049 (15)0.015 (2)
C170.035 (3)0.050 (4)0.034 (3)0.007 (3)0.008 (2)0.009 (3)
C180.038 (3)0.041 (4)0.044 (3)0.007 (3)0.001 (3)0.001 (3)
C190.025 (2)0.028 (3)0.021 (2)0.001 (2)0.0068 (19)0.001 (2)
C200.018 (2)0.025 (3)0.015 (2)0.000 (2)0.0010 (18)0.004 (2)
C210.019 (2)0.021 (3)0.025 (2)0.001 (2)0.0010 (19)0.002 (2)
C220.026 (3)0.033 (3)0.020 (2)0.002 (2)0.006 (2)0.003 (2)
C230.016 (2)0.031 (3)0.021 (2)0.007 (2)0.0101 (19)0.012 (2)
C240.020 (2)0.025 (3)0.029 (3)0.001 (2)0.001 (2)0.002 (2)
O250.0294 (19)0.026 (2)0.043 (2)0.0087 (17)0.0114 (15)0.0002 (17)
C260.027 (3)0.031 (3)0.040 (3)0.000 (2)0.010 (2)0.014 (3)
O270.0312 (19)0.038 (2)0.033 (2)0.0068 (18)0.0115 (15)0.0093 (18)
Geometric parameters (Å, º) top
C1—O21.239 (6)C12—C181.518 (7)
C1—N31.339 (6)O13—C141.429 (5)
C1—C61.521 (6)C14—C151.512 (6)
N3—C51.452 (7)C14—H141.0
N3—C41.462 (6)C15—O161.425 (6)
C4—H4A0.98C15—H15A0.99
C4—H4B0.98C15—H15B0.99
C4—H4C0.98O16—H160.84
C4—H4D0.98C17—H17A0.98
C4—H4E0.98C17—H17B0.98
C4—H4F0.98C17—H17C0.98
C5—H5A0.98C18—H18A0.98
C5—H5B0.98C18—H18B0.98
C5—H5C0.98C18—H18C0.98
C6—C71.533 (6)C19—C241.373 (6)
C6—H6A0.99C19—C201.398 (7)
C6—H6B0.99C19—H190.95
C7—C81.508 (6)C20—C211.394 (6)
C7—C201.530 (6)C21—C221.403 (6)
C7—H71.0C21—H210.95
C8—C91.317 (6)C22—C231.366 (7)
C8—H80.95C22—H220.95
C9—C101.496 (6)C23—C241.379 (6)
C9—H90.95C23—O271.387 (6)
C10—O111.435 (5)C24—O251.381 (6)
C10—C141.535 (6)O25—C261.439 (5)
C10—H101.0C26—O271.440 (6)
O11—C121.422 (5)C26—H26A0.99
C12—O131.440 (5)C26—H26B0.99
C12—C171.509 (7)
O2—C1—N3121.7 (4)C17—C12—C18112.3 (4)
O2—C1—C6120.6 (4)C14—O13—C12109.1 (3)
N3—C1—C6117.7 (4)O13—C14—C15109.8 (4)
C1—N3—C5124.4 (4)O13—C14—C10101.7 (3)
C1—N3—C4119.6 (4)C15—C14—C10115.9 (4)
C5—N3—C4116.0 (4)O13—C14—H14109.7
N3—C4—H4A109.5C15—C14—H14109.7
N3—C4—H4B109.5C10—C14—H14109.7
H4A—C4—H4B109.5O16—C15—C14111.2 (4)
N3—C4—H4C109.5O16—C15—H15A109.4
H4A—C4—H4C109.5C14—C15—H15A109.4
H4B—C4—H4C109.5O16—C15—H15B109.4
N3—C4—H4D109.5C14—C15—H15B109.4
N3—C4—H4E109.5H15A—C15—H15B108.0
H4D—C4—H4E109.5C15—O16—H16109.5
N3—C4—H4F109.5C12—C17—H17A109.5
H4D—C4—H4F109.5C12—C17—H17B109.5
H4E—C4—H4F109.5H17A—C17—H17B109.5
N3—C5—H5A109.5C12—C17—H17C109.5
N3—C5—H5B109.5H17A—C17—H17C109.5
H5A—C5—H5B109.5H17B—C17—H17C109.5
N3—C5—H5C109.5C12—C18—H18A109.5
H5A—C5—H5C109.5C12—C18—H18B109.5
H5B—C5—H5C109.5H18A—C18—H18B109.5
C1—C6—C7112.6 (4)C12—C18—H18C109.5
C1—C6—H6A109.1H18A—C18—H18C109.5
C7—C6—H6A109.1H18B—C18—H18C109.5
C1—C6—H6B109.1C24—C19—C20117.7 (4)
C7—C6—H6B109.1C24—C19—H19121.1
H6A—C6—H6B107.8C20—C19—H19121.1
C8—C7—C20110.0 (3)C21—C20—C19120.1 (4)
C8—C7—C6114.0 (4)C21—C20—C7120.0 (4)
C20—C7—C6109.4 (4)C19—C20—C7120.0 (4)
C8—C7—H7107.7C20—C21—C22121.2 (4)
C20—C7—H7107.7C20—C21—H21119.4
C6—C7—H7107.7C22—C21—H21119.4
C9—C8—C7127.7 (4)C23—C22—C21117.4 (4)
C9—C8—H8116.1C23—C22—H22121.3
C7—C8—H8116.1C21—C22—H22121.3
C8—C9—C10125.1 (4)C22—C23—C24121.5 (4)
C8—C9—H9117.4C22—C23—O27129.1 (4)
C10—C9—H9117.4C24—C23—O27109.4 (4)
O11—C10—C9110.1 (4)C19—C24—C23122.1 (5)
O11—C10—C14101.4 (4)C19—C24—O25127.6 (4)
C9—C10—C14116.1 (4)C23—C24—O25110.3 (4)
O11—C10—H10109.6C24—O25—C26105.3 (4)
C9—C10—H10109.6O25—C26—O27107.3 (4)
C14—C10—H10109.6O25—C26—H26A110.3
C12—O11—C10107.2 (3)O27—C26—H26A110.3
O11—C12—O13105.9 (3)O25—C26—H26B110.3
O11—C12—C17111.5 (4)O27—C26—H26B110.3
O13—C12—C17108.3 (4)H26A—C26—H26B108.5
O11—C12—C18108.7 (4)C23—O27—C26105.6 (3)
O13—C12—C18109.9 (4)
O2—C1—N3—C5176.1 (5)C9—C10—C14—C1536.9 (6)
C6—C1—N3—C53.8 (7)O13—C14—C15—O16159.9 (3)
O2—C1—N3—C47.7 (7)C10—C14—C15—O1685.6 (5)
C6—C1—N3—C4172.4 (4)C24—C19—C20—C210.8 (6)
O2—C1—C6—C715.6 (6)C24—C19—C20—C7178.7 (4)
N3—C1—C6—C7164.4 (4)C8—C7—C20—C21124.5 (4)
C1—C6—C7—C866.5 (5)C6—C7—C20—C21109.5 (5)
C1—C6—C7—C20169.8 (4)C8—C7—C20—C1955.0 (6)
C20—C7—C8—C9121.4 (5)C6—C7—C20—C1971.0 (5)
C6—C7—C8—C91.9 (7)C19—C20—C21—C220.6 (6)
C7—C8—C9—C10178.2 (4)C7—C20—C21—C22179.0 (4)
C8—C9—C10—O116.0 (7)C20—C21—C22—C230.3 (7)
C8—C9—C10—C14108.5 (5)C21—C22—C23—C240.4 (7)
C9—C10—O11—C12159.5 (4)C21—C22—C23—O27179.2 (4)
C14—C10—O11—C1236.0 (4)C20—C19—C24—C230.9 (7)
C10—O11—C12—O1321.5 (5)C20—C19—C24—O25178.9 (4)
C10—O11—C12—C1796.1 (5)C22—C23—C24—C190.7 (7)
C10—O11—C12—C18139.5 (4)O27—C23—C24—C19178.9 (4)
O11—C12—O13—C143.5 (5)C22—C23—C24—O25179.0 (4)
C17—C12—O13—C14123.2 (4)O27—C23—C24—O250.6 (5)
C18—C12—O13—C14113.8 (4)C19—C24—O25—C26172.4 (5)
C12—O13—C14—C1598.5 (4)C23—C24—O25—C269.4 (5)
C12—O13—C14—C1024.8 (5)C24—O25—C26—O2714.4 (5)
O11—C10—C14—O1336.5 (4)C22—C23—O27—C26172.0 (5)
C9—C10—C14—O13155.8 (4)C24—C23—O27—C268.4 (5)
O11—C10—C14—C1582.5 (4)O25—C26—O27—C2314.1 (5)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C19–C24 benzene ring.
D—H···AD—HH···AD···AD—H···A
O16—H16···O20.841.992.810 (5)166
C14—H14···O13i1.002.433.253 (6)139
C5—H5A···O16ii0.982.553.417 (7)147
C22—H22···O2iii0.952.553.417 (5)152
C21—H21···Cgiv0.952.983.794 (4)145
Symmetry codes: (i) x+1, y+1/2, z; (ii) x, y+1, z; (iii) x+1, y+1/2, z+1; (iv) x+1, y1/2, z+1.
 

Acknowledgements

We also thank Professor S. Ohba (Keio University, Japan) for his advice.

Funding information

Funding for this research was provided by: Keio Gijuku Fukuzawa Memorial Fund for the Advancement of Education and Research.

References

First citationBruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationDoyle, T. J., Hendrix, M. & Haseltine, J. (1995). Tetrahedron Lett. 35, 8295–8298.  CrossRef Google Scholar
First citationDoyle, T. J., VanDerveer, D. & Haseltine, J. (1994). Tetrahedron Lett. 36, 6197–6200.  CrossRef Google Scholar
First citationGelas, J. & Horton, D. (1975). Carbohydr. Res. 45, 181–195.  CrossRef Google Scholar
First citationGroom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationIshii, K., Seki, Y., Ishibashi, M., Sato, T. & Chida, N. (2018). preparation.  Google Scholar
First citationMacrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationRotherham, L. W. & Semple, J. E. (1998). J. Org. Chem. 63, 6667–6672.  CrossRef Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationVijayasaradhi, S., Aidhen, I. S. & Varghese, B. (2003). Carbohydr. Res. 338, 2899–2903.  CrossRef Google Scholar
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWuts, P. G. M. (2014). Green's Protective Groups in Organic Synthesis, 5th ed., pp. 385–456, 465–468 and 545–552. New York: John Wiley & Sons Inc.  Google Scholar

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